A part of the reason, at least, is because they share a child together. There was at this time, even in Tom and Daisy's social set, a strong prejudice against divorced couples; especially couples with children. Daisy, especially, would have risked serious social scorn. Even though Tom kept a mistress, if he were discreet enough the prevailing idea among their friends would be that they should avoid divorce at all costs.
Another reason is that girls like Daisy "didn't marry poor boys," as she had said all those years ago in St. Louis. Gatsby, though he had made piles of money, was still the social parvenu -- the nouveau riche. For Daisy, even if she loved Gatsby still (or ever, and that is debatable), divorcing Tom and marrying Gatsby would be a step down for her socially. Again, the opinion of others would be paramount to Daisy; it was the only social currency and standard of worth she understood.
Gatsy made several blunders in regards to Daisy, however, that didn't help his already hopeless situation. He spent money like the new rich often do: with obscene abandon. His overly lavish lifestyle, and, especially, his parties full of parasites and dubious hangers-on, would have lessened Gatsby's social status among Tom and Daisy's friends. And Tom and Daisy's friends' opinions were what mattered, ultimately, to Daisy. Gatsby also told some exaggerations and some outright lies about his past, and tried very hard to be something he was not (a product of a wealthy family). If Gatsby were to have any chance with Daisy (and, again, that is debatable) he would much better have owned up to his past and been proud of his humble origins.
But Gatsby was a bootlegger, and lived by criminal activity. It was in his nature to lie and to cheat, and he thought by wishing and saying enough that he had a similar background to the man Daisy did marry, Tom, that it would make it so. Gatsby found out, too late, that this was never going to be the case.
Also, Gatsby was far too intense in his love, which was almost worship, of Daisy. This, understandably, frightened Daisy enough that her philandering, blowhard husband -- the "devil she knew" -- was preferable to the volatile, lying, criminal Gatsby. In the end it didn't matter how charming Gatsby was; he was not the man Daisy would choose.
If Tom and Daisy ever had a close, passionate, and most of all loving relationship, it is at best difficult for the reader to make that discovery. ( Fitzgerald's intent) Tom and Daisy are similar because social status and material wealth are liken to the air they breathe. What is so disturbing between Tom and Daisy's relationship is their perversion of the most powerful connection between a man and a woman, passionate love. Fitzgerald allows the reader to witness the perversion of this beautiful and intimate connection between two human beings through Tom and Daisy's love of 'things and 'image' not eachother. Tom and Daisy stay together not because they love eachother, but because they love illusion more than they love the truth.
Both Tom and Daisy are from the same social class. Even though their marriage is not necessarily a good one, it is socially acceptable and allows both of them to live among the rich and elite. To Daisy, this is obviously more important than romantic love. In the end, she rejects Gatsby and does not even bother to come to his funeral. She and Tom simply disappear on a trip for a while. As Nick notes, they were careless people and neither one of them really took responsibility for their actions. Because they had money, they could afford to let other people pick up their messes for them. This love of money and status over the love for people is what sends Nick back to the Midwest at the end of the novel.
Sfwriter offers a wonderful perspective for your question, I wish someone had explained it so well when I read The Great Gatsby back in High School, it offers a sense of closure to hear a solid argument for why Daisy would never have chosen Gatsby.
It should be noted however that it was Louisville, Kentucky where Daisy and Gatsby met; not St. Louis. Louisville boasts a rich, historical backdrop that is ideal for a story set in The Roaring Twenties (though it was still World War I when Gatsby and Daisy met, of course). Just think about it; gambling on horses at Church Hill Downs during Derby, tossing back moonshine during prohibition (Kentucky is home to the Bourbon capital of the world, and Louisville is famous for it's whiskey and tabbaco), strolling through the moneyed streets of The Highlands gazing up enviously at the enormous, old houses lining the blue grass there . . .nothing says Roaring Twenties more!
I grew up in Louisville, so The Great Gatsby has special significance to me. The setting of Louisville was central in our classroom discussions because it was local, so everybody could really get into the world crafted by F. Scott Fitzgerald, because we knew where all these places were.